S3_fit_models.R

#setwd("") # set directory to the folder where the folders "data", "models" and "panels" are
library(Hmsc)

load(file = "models/unfitted_models") #models, modelnames


# samples_list = c(5,250,250,250,250)
# thin_list = c(1,1,10,100,1000)

samples_list = c(5,50, 250, 250, 250)
thin_list = c(1,10, 100, 1000, 10000)
nChains = 4
for(Lst in 1:length(samples_list)){
  thin = thin_list[Lst]
  samples = samples_list[Lst]
  print(paste0("thin = ",as.character(thin),"; samples = ", as.character(samples)))
  nm = length(models)
  for (model in 1:nm) {
    print(paste0("model = ",modelnames[model]))
    m = models[[model]]
    m = sampleMcmc(m, samples = samples, thin=thin,
                   adaptNf=rep(ceiling(0.4*samples*thin),m$nr), 
                   transient = ceiling(0.5*samples*thin),
                   nChains = nChains,
                   nParallel = nChains) 
    models[[model]] = m
  }
  filename = paste("models/models_thin_", as.character(thin),
                   "_samples_", as.character(samples),
                   "_chains_",as.character(nChains),
                   ".Rdata",sep = "")
  save(models,modelnames,file=filename)
}